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An environmentally compatible method for controlling sapstain fungi in wood was evaluated, using a combination of chitosan and an albino strain of <i>Trichoderma harzianum</i>, a biological control agent (BCA). The growth and penetration into the wood of the sapstain fungi <i>Ophiostoma piceae</i>, <i>Leptographium procerum,</i> and <i>Sphaeropsis sapinea</i> were assessed in radiata pine wafers treated with chitosan and BCA, both alone and in combination. Several mycological and microscopic techniques were used, including a <i>gfp</i> (green fluorescent protein) transformed strain of <i>O. piceae</i> for assessing the depth of penetration in the wood samples. The synergy between the chitosan and BCA was evident, and for two tested fungi, only the combination of chitosan and BCA afforded protection. The synnemata (recognized by erect conidiogenous cells bearing conidia) was observed on the surface of the wafers inoculated with <i>L. procerum</i> and <i>O. piceae</i>, but the hyphae were unable to penetrate and melanise. The results suggest that the limited ability of chitosan to penetrate deeply into the wood was compensated by the fast growth of <i>T. harzianum</i> in the inner wood.